Mutagenetix > Incidental Mutation

Incidental Mutation 'R5137:Vps53'

475469

Institutional Source

Beutler Lab

Gene Symbol

Vps53

Ensembl Gene

ENSMUSG00000017288

Gene Name

VPS53 GARP complex subunit

Synonyms

2310040I21Rik, 3100002B05Rik, 2010002A08Rik

MMRRC Submission

042723-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5137 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

75937052-76070464 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 76057074 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 57 (S57P)

Ref Sequence

ENSEMBL: ENSMUSP00000130499 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000163878] [ENSMUST00000166752] [ENSMUST00000167114] [ENSMUST00000169734] [ENSMUST00000170730]

AlphaFold

Q8CCB4

Predicted Effect

probably damaging
Transcript: ENSMUST00000056601
AA Change: S57P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: S57P

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	5.9e-11	PFAM
Pfam:Vps53_N	39	453	1.9e-176	PFAM
low complexity region	520	533	N/A	INTRINSIC
low complexity region	820	832	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000094015
AA Change: S57P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: S57P

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	96	6.2e-21	PFAM
Pfam:Vps53_N	93	424	1.4e-133	PFAM
low complexity region	491	504	N/A	INTRINSIC
low complexity region	791	803	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000108419
AA Change: S57P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: S57P

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	224	4e-11	PFAM
Pfam:Vps53_N	39	233	5.2e-87	PFAM
Pfam:Vps53_N	226	276	1.6e-14	PFAM
low complexity region	343	356	N/A	INTRINSIC
low complexity region	643	655	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140886

Predicted Effect

probably benign
Transcript: ENSMUST00000163878

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166084

Predicted Effect

probably benign
Transcript: ENSMUST00000166436

SMART Domains

Protein: ENSMUSP00000131387
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
Pfam:DUF2450	1	155	1.6e-8	PFAM
Pfam:Vps53_N	1	204	6.1e-91	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000166752
AA Change: S57P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: S57P

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	8.2e-12	PFAM
Pfam:Vps53_N	39	230	6e-87	PFAM
Pfam:Vps53_N	226	405	1.4e-60	PFAM
low complexity region	472	485	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000167114
AA Change: S57P

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: S57P

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	101	1.2e-21	PFAM
Pfam:Vps53_N	104	176	3.1e-15	PFAM
low complexity region	243	256	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000169734
AA Change: S57P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: S57P

Domain	Start	End	E-Value	Type
Pfam:DUF2450	5	225	5.1e-12	PFAM
Pfam:Vps53_N	39	329	1e-137	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170143

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169532

Predicted Effect

probably benign
Transcript: ENSMUST00000170730

SMART Domains

Protein: ENSMUSP00000127364
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	54	123	3e-34	PFAM

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 94.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E12.5 with trophoblast cell hyperplasia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad9	T	C	3: 36,123,920 (GRCm39)	V75A	probably benign	Het
Ace	G	C	11: 105,865,652 (GRCm39)	W628C	probably damaging	Het
Adh4	T	C	3: 138,127,996 (GRCm39)	S141P	probably benign	Het
Apob	T	C	12: 8,061,384 (GRCm39)	Y3256H	possibly damaging	Het
B3galnt1	G	T	3: 69,482,282 (GRCm39)	N326K	probably benign	Het
Bltp3a	T	G	17: 28,095,964 (GRCm39)		probably null	Het
Catsperb	T	C	12: 101,516,070 (GRCm39)	F569L	probably damaging	Het
Cecr2	A	G	6: 120,732,478 (GRCm39)	I225V	probably benign	Het
Cox5b	A	G	1: 36,731,510 (GRCm39)		probably null	Het
Crybg1	T	C	10: 43,834,332 (GRCm39)	D1953G	probably damaging	Het
Dnaaf5	C	T	5: 139,167,215 (GRCm39)	T707M	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Ebf1	G	A	11: 44,882,295 (GRCm39)	R409Q	probably damaging	Het
Eef2k	G	A	7: 120,484,645 (GRCm39)	A256T	probably damaging	Het
Eef2k	C	A	7: 120,484,646 (GRCm39)	A256D	probably damaging	Het
Evl	C	G	12: 108,647,781 (GRCm39)	T294S	probably benign	Het
Eya2	T	C	2: 165,573,548 (GRCm39)	Y288H	probably damaging	Het
Ezh2	A	T	6: 47,509,014 (GRCm39)		probably null	Het
Fam171a1	T	C	2: 3,226,426 (GRCm39)	Y395H	probably benign	Het
Gas2l3	C	A	10: 89,249,837 (GRCm39)	R427L	probably damaging	Het
Gli2	T	A	1: 118,783,233 (GRCm39)	I91F	probably damaging	Het
Gm4884	T	C	7: 40,692,318 (GRCm39)	S96P	probably damaging	Het
Gprc5d	T	A	6: 135,093,031 (GRCm39)	D292V	probably benign	Het
Herc1	A	G	9: 66,355,505 (GRCm39)	K2252R	probably benign	Het
Il1rl1	A	T	1: 40,489,285 (GRCm39)	M346L	probably benign	Het
Kcna5	A	T	6: 126,510,946 (GRCm39)	V394D	probably damaging	Het
Kcng4	A	T	8: 120,352,617 (GRCm39)	M431K	possibly damaging	Het
Kifbp	A	T	10: 62,414,020 (GRCm39)	V46E	probably damaging	Het
Large1	A	G	8: 73,774,937 (GRCm39)	F258L	possibly damaging	Het
Mapkbp1	T	A	2: 119,852,662 (GRCm39)	C1001S	probably damaging	Het
Micu1	A	G	10: 59,663,054 (GRCm39)	Q328R	probably benign	Het
Mmp11	G	A	10: 75,761,290 (GRCm39)	P437S	probably damaging	Het
Msh6	T	A	17: 88,287,716 (GRCm39)	F119I	possibly damaging	Het
Myo6	A	G	9: 80,149,531 (GRCm39)	E159G	probably damaging	Het
Negr1	T	A	3: 156,721,833 (GRCm39)	Y136N	probably damaging	Het
Nol9	T	A	4: 152,130,428 (GRCm39)	C321S	probably damaging	Het
Nos1	T	C	5: 118,043,378 (GRCm39)	F551S	probably benign	Het
Nup153	C	A	13: 46,837,629 (GRCm39)	G1198C	probably damaging	Het
Omd	T	C	13: 49,743,552 (GRCm39)	S201P	probably benign	Het
Or1e16	AGCGGTCGTAGGC	AGC	11: 73,286,480 (GRCm39)		probably null	Het
Or1e35	T	C	11: 73,797,452 (GRCm39)	I289V	probably damaging	Het
Or4c120	C	A	2: 89,000,744 (GRCm39)	V271F	probably benign	Het
Or51l14	A	G	7: 103,100,919 (GRCm39)	Y125C	probably damaging	Het
Or51l14	C	A	7: 103,100,920 (GRCm39)	Y125*	probably null	Het
Oxct1	G	T	15: 4,064,832 (GRCm39)	A57S	probably benign	Het
Pcdhga7	T	G	18: 37,850,433 (GRCm39)	S813R	probably damaging	Het
Pcmtd2	A	T	2: 181,496,787 (GRCm39)	I255F	possibly damaging	Het
Pdk1	T	G	2: 71,713,913 (GRCm39)	M186R	possibly damaging	Het
Pelp1	T	C	11: 70,285,925 (GRCm39)	T648A	probably damaging	Het
Phldb2	A	T	16: 45,628,621 (GRCm39)	S570R	possibly damaging	Het
Pramel16	T	A	4: 143,675,690 (GRCm39)	T379S	probably benign	Het
Ptprj	T	C	2: 90,299,992 (GRCm39)	T270A	possibly damaging	Het
Reln	C	T	5: 22,160,179 (GRCm39)	G2130D	probably damaging	Het
Rims1	A	T	1: 22,358,844 (GRCm39)	Y663*	probably null	Het
Rit2	T	C	18: 31,286,817 (GRCm39)	T123A	probably benign	Het
Rmdn2	A	T	17: 79,975,418 (GRCm39)	E302D	probably benign	Het
Ryr1	T	C	7: 28,801,283 (GRCm39)	E827G	possibly damaging	Het
Siglec1	C	T	2: 130,923,264 (GRCm39)	G494R	probably damaging	Het
Slc16a14	T	A	1: 84,890,318 (GRCm39)	Y329F	probably damaging	Het
Slc35d1	A	T	4: 103,071,978 (GRCm39)	L8Q	possibly damaging	Het
Smpdl3a	C	T	10: 57,677,163 (GRCm39)	S57L	possibly damaging	Het
Snx9	T	C	17: 5,978,528 (GRCm39)	V566A	probably damaging	Het
Spaca1	A	T	4: 34,029,095 (GRCm39)	I126N	probably damaging	Het
Spred1	T	G	2: 116,994,052 (GRCm39)	I94S	probably damaging	Het
Tardbp	T	C	4: 148,706,494 (GRCm39)	D105G	possibly damaging	Het
Tet2	T	C	3: 133,182,326 (GRCm39)	S1213G	probably benign	Het
Trak1	A	T	9: 121,196,121 (GRCm39)		probably benign	Het
Trem3	G	A	17: 48,556,756 (GRCm39)	V76M	possibly damaging	Het
Ttc13	G	T	8: 125,421,674 (GRCm39)	Y250*	probably null	Het
Ttll5	T	G	12: 85,969,819 (GRCm39)	S714R	possibly damaging	Het
Ube2l6	T	G	2: 84,633,220 (GRCm39)		probably null	Het
Ubr3	T	C	2: 69,803,679 (GRCm39)	S1090P	probably damaging	Het
Vezt	T	C	10: 93,806,372 (GRCm39)	T680A	probably benign	Het
Virma	A	G	4: 11,546,297 (GRCm39)	K1762E	probably damaging	Het
Vwa7	G	T	17: 35,236,822 (GRCm39)	D130Y	probably damaging	Het
Vwa8	T	G	14: 79,302,342 (GRCm39)	F1004V	probably damaging	Het
Zfp35	A	T	18: 24,137,194 (GRCm39)	K513*	probably null	Het
Zfp384	ACAGCAGCAGCAGCAGCAGCAGC	ACAGCAGCAGCAGCAGCAGC	6: 125,013,472 (GRCm39)		probably benign	Het
Zfp521	C	A	18: 13,978,505 (GRCm39)	C636F	probably damaging	Het

Other mutations in Vps53

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00475:Vps53	APN	11	75,967,861 (GRCm39)	splice site	probably null
IGL01596:Vps53	APN	11	75,953,863 (GRCm39)	missense	probably damaging	1.00
IGL01655:Vps53	APN	11	75,953,860 (GRCm39)	missense	probably damaging	0.97
IGL02275:Vps53	APN	11	75,937,949 (GRCm39)	missense	probably benign	0.03
IGL02321:Vps53	APN	11	75,939,364 (GRCm39)	missense	possibly damaging	0.60
IGL02581:Vps53	APN	11	75,992,883 (GRCm39)	missense	probably damaging	0.99
IGL02821:Vps53	APN	11	76,027,143 (GRCm39)	splice site	probably benign
IGL02958:Vps53	APN	11	76,008,537 (GRCm39)	missense	probably damaging	1.00
IGL03001:Vps53	APN	11	76,029,150 (GRCm39)	missense	probably damaging	1.00
PIT4519001:Vps53	UTSW	11	76,007,999 (GRCm39)	missense	probably damaging	1.00
R0257:Vps53	UTSW	11	76,068,211 (GRCm39)	intron	probably benign
R0391:Vps53	UTSW	11	76,012,405 (GRCm39)	missense	probably benign	0.31
R0421:Vps53	UTSW	11	75,973,496 (GRCm39)	missense	probably damaging	1.00
R0882:Vps53	UTSW	11	75,973,485 (GRCm39)	missense	probably damaging	1.00
R2509:Vps53	UTSW	11	75,957,661 (GRCm39)	missense	possibly damaging	0.49
R3622:Vps53	UTSW	11	76,008,609 (GRCm39)	missense	probably benign	0.00
R5338:Vps53	UTSW	11	75,972,034 (GRCm39)	missense	probably damaging	1.00
R5756:Vps53	UTSW	11	75,983,156 (GRCm39)	splice site	probably benign
R5786:Vps53	UTSW	11	75,953,833 (GRCm39)	missense	probably benign	0.08
R5961:Vps53	UTSW	11	75,939,316 (GRCm39)	missense	probably damaging	1.00
R6059:Vps53	UTSW	11	75,957,693 (GRCm39)	missense	possibly damaging	0.57
R6273:Vps53	UTSW	11	75,992,844 (GRCm39)	missense	probably benign	0.16
R6490:Vps53	UTSW	11	75,967,881 (GRCm39)	missense	probably benign	0.03
R6657:Vps53	UTSW	11	76,025,253 (GRCm39)	missense	probably damaging	1.00
R6671:Vps53	UTSW	11	76,025,332 (GRCm39)	missense	probably damaging	1.00
R6772:Vps53	UTSW	11	76,070,324 (GRCm39)	start codon destroyed	probably null
R7378:Vps53	UTSW	11	75,967,900 (GRCm39)	missense	possibly damaging	0.88
R7735:Vps53	UTSW	11	75,937,962 (GRCm39)	missense	probably damaging	1.00
R8066:Vps53	UTSW	11	76,027,133 (GRCm39)	missense	probably damaging	1.00
Z1177:Vps53	UTSW	11	76,027,024 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- CTGGCCAAAGAATCAAGCTC -3'
(R):5'- GTTCAAAGAATGGACATACATGCC -3'

Sequencing Primer
(F):5'- GAATCAAGCTCTTTGCCATAGAG -3'
(R):5'- AGAATGGACATACATGCCTACAC -3'

Posted On

2017-04-24